Genomics and Phylogenetic Studies

NEXCISION is a Python tool for exact removal of genomic regions from NEXUS matrices, validated for correctness, safety, and scalability in microbial phylogenomics.

This paper introduces a parallel and scalable implementation of the balanced minimum evolution algorithm for large-scale phylogenetic inference, achieving significant speedup and memory efficiency.

PlasChain improves long plasmid reconstruction from metagenome assemblies by addressing fragmentation and false positives, outperforming existing methods in recovering long plasmids.

The paper presents 320 nearly-complete East Asian genome assemblies, revealing new genetic diversity and structural variations not present in existing global pangenomes.

This paper introduces a variational inference method for Bayesian phylogenetic reconstruction, showing faster speeds than traditional Bayesian methods on real-world datasets.

ImpuT2T patches gaps in HiFi assemblies using pangenomes, improving quality over existing methods.

SyntenyPair Explorer provides an interactive, browser-based tool for visualizing synteny between two genomes without requiring installation or server infrastructure.

PhyloRBT detects reference bias in phylogenomic datasets by comparing locus reconstructions across multiple reference genomes, identifying biased loci that affect species tree inference.

Pansoma improves somatic variant calling using pangenome graphs, enhancing accuracy by avoiding reference bias and preserving graph-specific variant representations.

This paper introduces a graph-theoretic framework to uniquely represent cross-gene branch identities in phylogenomic data, ensuring consistent and auditable comparative analyses.

MeioBIOME is a Snakemake pipeline for analyzing holobiont metagenomes from single meiofaunal specimens, generating host-associated MAGs and SCGs.

The paper introduces an automated pipeline for whole-genome sequencing analysis of microbial pesticides to improve hazard characterization and risk assessment.

VizR provides an interactive web platform for end-to-end RNA-seq analysis and visualization in plant biology, reducing technical barriers through automation and integration.

PhytoFam automates plant gene family analysis through a Nextflow pipeline, integrating multiple tools for homolog detection, orthology assignment, and phylogenetic reconstruction.

GraTools is a command-line tool for manipulating pangenome variation graphs, enabling efficient subgraph extraction, sequence retrieval, and analysis of genomic diversity.

neissflow is a Nextflow pipeline for analyzing Neisseria gonorrhoeae genomes, achieving high accuracy in species identification, AMR profiling, and phylogenetic analysis.

Hobrac automates reference genome selection and structural comparison to visualize synteny, improving genome assembly validation and evolutionary analysis.

The paper shows that error-correction objectives for perfect phylogenies are statistically inconsistent, often favoring incorrect trees over the true one in simulated data.

460 haplotypes from 230 genomes, selected to maximize common-variant coverage, capture 99.43% of All of Us common small variants and halve structurally unreliable regions and base errors versus HPRC1.

MagicLamp provides a toolkit and web server for targeted microbial function annotation using curated HMMs, enabling sensitive and specific gene annotation for specialized processes.

The paper shows that contamination of rRNA databases with LSU sequences leads to incorrect taxonomic assignments in metagenomes and metatranscriptomes, and provides a cleaned database and tool to address this issue.

fastCDS maps protein domains to genomic coordinates efficiently, enabling rapid analysis of exonic architecture and variant interpretation.

This paper introduces a hierarchical clock-mixture model for Bayesian phylogenetic dating to better handle uncertainty in clock choice and improve timescale estimation.

The paper presents the first HiFi long-read assembled genome of the dipluran species Occasjapyx japonicus, providing a high-quality reference for comparative and evolutionary studies.

Panomap maps raw nanopore signals to pangenome variation graphs, improving mapping accuracy and reducing reference bias compared to linear-reference methods.

Evo 2 7B assigns higher perplexity to plant gene alleles carrying randomly simulated single-nucleotide substitutions than to those observed in vivo, in Arabidopsis and rice; significant but small effect.

This paper introduces grapHiC, a contrastive learning framework for reference-free haplotype phasing in de novo genome assembly, achieving results comparable to state-of-the-art methods.

This paper reports the annotation of three tiger beetle genomes, providing draft reference genomes for evolutionary and conservation studies.

This paper develops a DNA extraction protocol for museum-grade insects, enabling long-read sequencing, phylogenetics, and methylation profiling from degraded samples.